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A complete tool set for molecular QTL discovery and analysis
Population scale studies combining genetic information with molecular phenotypes (for example, gene expression) have become a standard to dissect the effects of genetic variants onto organismal phenotypes. These kinds of data sets require powerful, fast and versatile methods able to discover molecul...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454369/ https://www.ncbi.nlm.nih.gov/pubmed/28516912 http://dx.doi.org/10.1038/ncomms15452 |
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author | Delaneau, Olivier Ongen, Halit Brown, Andrew A. Fort, Alexandre Panousis, Nikolaos I. Dermitzakis, Emmanouil T. |
author_facet | Delaneau, Olivier Ongen, Halit Brown, Andrew A. Fort, Alexandre Panousis, Nikolaos I. Dermitzakis, Emmanouil T. |
author_sort | Delaneau, Olivier |
collection | PubMed |
description | Population scale studies combining genetic information with molecular phenotypes (for example, gene expression) have become a standard to dissect the effects of genetic variants onto organismal phenotypes. These kinds of data sets require powerful, fast and versatile methods able to discover molecular Quantitative Trait Loci (molQTL). Here we propose such a solution, QTLtools, a modular framework that contains multiple new and well-established methods to prepare the data, to discover proximal and distal molQTLs and, finally, to integrate them with GWAS variants and functional annotations of the genome. We demonstrate its utility by performing a complete expression QTL study in a few easy-to-perform steps. QTLtools is open source and available at https://qtltools.github.io/qtltools/. |
format | Online Article Text |
id | pubmed-5454369 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-54543692017-06-07 A complete tool set for molecular QTL discovery and analysis Delaneau, Olivier Ongen, Halit Brown, Andrew A. Fort, Alexandre Panousis, Nikolaos I. Dermitzakis, Emmanouil T. Nat Commun Article Population scale studies combining genetic information with molecular phenotypes (for example, gene expression) have become a standard to dissect the effects of genetic variants onto organismal phenotypes. These kinds of data sets require powerful, fast and versatile methods able to discover molecular Quantitative Trait Loci (molQTL). Here we propose such a solution, QTLtools, a modular framework that contains multiple new and well-established methods to prepare the data, to discover proximal and distal molQTLs and, finally, to integrate them with GWAS variants and functional annotations of the genome. We demonstrate its utility by performing a complete expression QTL study in a few easy-to-perform steps. QTLtools is open source and available at https://qtltools.github.io/qtltools/. Nature Publishing Group 2017-05-18 /pmc/articles/PMC5454369/ /pubmed/28516912 http://dx.doi.org/10.1038/ncomms15452 Text en Copyright © 2017, The Author(s) http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article's Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Delaneau, Olivier Ongen, Halit Brown, Andrew A. Fort, Alexandre Panousis, Nikolaos I. Dermitzakis, Emmanouil T. A complete tool set for molecular QTL discovery and analysis |
title | A complete tool set for molecular QTL discovery and analysis |
title_full | A complete tool set for molecular QTL discovery and analysis |
title_fullStr | A complete tool set for molecular QTL discovery and analysis |
title_full_unstemmed | A complete tool set for molecular QTL discovery and analysis |
title_short | A complete tool set for molecular QTL discovery and analysis |
title_sort | complete tool set for molecular qtl discovery and analysis |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454369/ https://www.ncbi.nlm.nih.gov/pubmed/28516912 http://dx.doi.org/10.1038/ncomms15452 |
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